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In this paper we present a wireless embedded system that performs active ultrasonic Structural Health Monitoring (SHM). The proposed Shimmer platform is an autonomous, battery-less system, powered by an energy harvester, which uses 16 piezoelectric sensors/actuators attached to the structure surface for SHM analysis. The collected data (≈4MB) are analyzed by the on-board DSP and the result is transmitted using the 6LoWPAN protocol with IEEE802.15.4 transceiver working at 915MHz. The significant challenge is running such intense analysis on the collected data with only energy harvesting as a power source. Our system combines solar and wind energy harvesters with a dynamic voltage and frequency scaling (DVFS) based task scheduling algorithm to optimize task execution with the available energy. Our solution enables Shimmer to perform 350 SHM analyses per day on average, corresponding to 80% improvement over a greedy based solution.